Job ID = 11240813 sra ファイルのダウンロード中... Completed: 265771K bytes transferred in 5 seconds (377509K bits/sec), in 1 file. sra ファイルのダウンロードが完了しました。 Read layout: SINGLE fastq に変換中... Read 7009007 spots for /home/okishinya/chipatlas/results/dm3/SRX4798861/SRR7965208.sra Written 7009007 spots for /home/okishinya/chipatlas/results/dm3/SRX4798861/SRR7965208.sra rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません rm: cannot remove `[DSE]RR*.fastq': そのようなファイルやディレクトリはありません fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:00:56 7009007 reads; of these: 7009007 (100.00%) were unpaired; of these: 5413374 (77.23%) aligned 0 times 1427804 (20.37%) aligned exactly 1 time 167829 (2.39%) aligned >1 times 22.77% overall alignment rate Time searching: 00:00:56 Overall time: 00:00:56 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 234433 / 1595633 = 0.1469 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Sun, 07 Oct 2018 20:47:10: # Command line: callpeak -t SRX4798861.bam -f BAM -g dm -n SRX4798861.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4798861.20 # format = BAM # ChIP-seq file = ['SRX4798861.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 07 Oct 2018 20:47:10: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:47:10: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:47:10: # Command line: callpeak -t SRX4798861.bam -f BAM -g dm -n SRX4798861.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4798861.05 # format = BAM # ChIP-seq file = ['SRX4798861.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 07 Oct 2018 20:47:10: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:47:10: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:47:10: # Command line: callpeak -t SRX4798861.bam -f BAM -g dm -n SRX4798861.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4798861.10 # format = BAM # ChIP-seq file = ['SRX4798861.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 07 Oct 2018 20:47:10: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:47:10: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:47:16: 1000000 INFO @ Sun, 07 Oct 2018 20:47:17: 1000000 INFO @ Sun, 07 Oct 2018 20:47:17: 1000000 INFO @ Sun, 07 Oct 2018 20:47:19: #1 tag size is determined as 51 bps INFO @ Sun, 07 Oct 2018 20:47:19: #1 tag size = 51 INFO @ Sun, 07 Oct 2018 20:47:19: #1 total tags in treatment: 1361200 INFO @ Sun, 07 Oct 2018 20:47:19: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:47:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:47:19: #1 tags after filtering in treatment: 1361200 INFO @ Sun, 07 Oct 2018 20:47:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:47:19: #1 finished! INFO @ Sun, 07 Oct 2018 20:47:19: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:47:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:47:19: #2 number of paired peaks: 1584 INFO @ Sun, 07 Oct 2018 20:47:19: start model_add_line... INFO @ Sun, 07 Oct 2018 20:47:19: start X-correlation... INFO @ Sun, 07 Oct 2018 20:47:19: end of X-cor INFO @ Sun, 07 Oct 2018 20:47:19: #2 finished! INFO @ Sun, 07 Oct 2018 20:47:19: #2 predicted fragment length is 166 bps INFO @ Sun, 07 Oct 2018 20:47:19: #2 alternative fragment length(s) may be 166 bps INFO @ Sun, 07 Oct 2018 20:47:19: #2.2 Generate R script for model : SRX4798861.10_model.r INFO @ Sun, 07 Oct 2018 20:47:19: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:47:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:47:19: #1 tag size is determined as 51 bps INFO @ Sun, 07 Oct 2018 20:47:19: #1 tag size = 51 INFO @ Sun, 07 Oct 2018 20:47:19: #1 total tags in treatment: 1361200 INFO @ Sun, 07 Oct 2018 20:47:19: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:47:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:47:19: #1 tags after filtering in treatment: 1361200 INFO @ Sun, 07 Oct 2018 20:47:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:47:19: #1 finished! INFO @ Sun, 07 Oct 2018 20:47:19: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:47:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:47:19: #1 tag size is determined as 51 bps INFO @ Sun, 07 Oct 2018 20:47:19: #1 tag size = 51 INFO @ Sun, 07 Oct 2018 20:47:19: #1 total tags in treatment: 1361200 INFO @ Sun, 07 Oct 2018 20:47:19: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:47:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:47:19: #1 tags after filtering in treatment: 1361200 INFO @ Sun, 07 Oct 2018 20:47:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:47:19: #1 finished! INFO @ Sun, 07 Oct 2018 20:47:19: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:47:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:47:19: #2 number of paired peaks: 1584 INFO @ Sun, 07 Oct 2018 20:47:19: start model_add_line... INFO @ Sun, 07 Oct 2018 20:47:19: start X-correlation... INFO @ Sun, 07 Oct 2018 20:47:19: end of X-cor INFO @ Sun, 07 Oct 2018 20:47:19: #2 finished! INFO @ Sun, 07 Oct 2018 20:47:19: #2 predicted fragment length is 166 bps INFO @ Sun, 07 Oct 2018 20:47:19: #2 alternative fragment length(s) may be 166 bps INFO @ Sun, 07 Oct 2018 20:47:19: #2.2 Generate R script for model : SRX4798861.20_model.r INFO @ Sun, 07 Oct 2018 20:47:19: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:47:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:47:19: #2 number of paired peaks: 1584 INFO @ Sun, 07 Oct 2018 20:47:19: start model_add_line... INFO @ Sun, 07 Oct 2018 20:47:19: start X-correlation... INFO @ Sun, 07 Oct 2018 20:47:19: end of X-cor INFO @ Sun, 07 Oct 2018 20:47:19: #2 finished! INFO @ Sun, 07 Oct 2018 20:47:19: #2 predicted fragment length is 166 bps INFO @ Sun, 07 Oct 2018 20:47:19: #2 alternative fragment length(s) may be 166 bps INFO @ Sun, 07 Oct 2018 20:47:19: #2.2 Generate R script for model : SRX4798861.05_model.r INFO @ Sun, 07 Oct 2018 20:47:19: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:47:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:47:22: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:47:23: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:47:23: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:47:24: #4 Write output xls file... SRX4798861.10_peaks.xls INFO @ Sun, 07 Oct 2018 20:47:24: #4 Write peak in narrowPeak format file... SRX4798861.10_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:47:24: #4 Write summits bed file... SRX4798861.10_summits.bed INFO @ Sun, 07 Oct 2018 20:47:24: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (231 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 20:47:24: #4 Write output xls file... SRX4798861.20_peaks.xls INFO @ Sun, 07 Oct 2018 20:47:24: #4 Write peak in narrowPeak format file... SRX4798861.20_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:47:24: #4 Write output xls file... SRX4798861.05_peaks.xls INFO @ Sun, 07 Oct 2018 20:47:24: #4 Write summits bed file... SRX4798861.20_summits.bed INFO @ Sun, 07 Oct 2018 20:47:24: Done! INFO @ Sun, 07 Oct 2018 20:47:25: #4 Write peak in narrowPeak format file... SRX4798861.05_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:47:25: #4 Write summits bed file... SRX4798861.05_summits.bed INFO @ Sun, 07 Oct 2018 20:47:25: Done! pass1 - making usageList (8 chroms): 2 millis pass2 - checking and writing primary data (31 records, 4 fields): 2 millis CompletedMACS2peakCalling pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (898 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。